Evaluating the accuracy of a functional SNP annotation system

Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to understanding human genetic variation. A key element in assessing role of a given SNP is determining if the variation is likely to result in change in function. The SNP Integration Tool (SNPit) is a comprehensive tool that integrates diverse, existing predictors of SNP functionality, providing the user with information for improved association study analysis. To evaluate the SNPit system, we developed an alternative gold standard to measure accuracy using sensitivity and specificity. The results of our evaluation demonstrated that our alternative gold standard produced encouraging results

Remote Data Retrieval for Bioinformatics Applications: An Agent Migration Approach

Some of the approaches have been developed to retrieve data automatically from one or multiple remote biological data sources. However, most of them require researchers to remain online and wait for returned results. The latter not only requires highly available network connection, but also may cause the network overload. Moreover, so far none of the existing approaches has been designed to address the following problems when retrieving the remote data in a mobile network environment: (1) the resources of mobile devices are limited; (2) network connection is relatively of low quality; and (3) mobile users are not always online. To address the aforementioned problems, we integrate an agent migration approach with a multi-agent system to overcome the high latency or limited bandwidth problem by moving their computations to the required resources or services. More importantly, the approach is fit for the mobile computing environments. Presented in this paper are also the system architecture, the migration strategy, as well as the security authentication of agent migration. As a demonstration, the remote data retrieval from GenBank was used to illustrate the feasibility of the proposed approach

Place- and age-responsive disaster risk reduction for Hong Kong: Collaborative Place Audit and Social Vulnerability Index for elders

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Assay platform for clinically relevant metallo-beta-lactamases

Metallo-β-lactamases (MBLs) are a growing threat to the use of almost all clinically used β-lactam antibiotics. The identification of broad-spectrum MBL inhibitors is hampered by the lack of a suitable screening platform, consisting of appropriate substrates and a set of clinically relevant MBLs. We report procedures for the preparation of a set of clinically relevant metallo-β-lactamases (i.e., NDM-1 (New Delhi MBL), IMP-1 (Imipenemase), SPM-1 (São Paulo MBL), and VIM-2 (Verona integron-encoded MBL)) and the identification of suitable fluorogenic substrates (umbelliferone-derived cephalosporins). The fluorogenic substrates were compared to chromogenic substrates (CENTA, nitrocefin, and imipenem), showing improved sensitivity and kinetic parameters. The efficiency of the fluorogenic substrates was exemplified by inhibitor screening, identifying 4-chloroisoquinolinols as potential pan MBL inhibitors

Biomedical informatics and translational medicine

Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics) may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records) and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians") can be essential members of translational medicine teams

Audio multicast by visible light communication for location information for the visually impaired

Visible Light Communication (VLC) is a new technology that may become an alternative choice for wireless communication in the future. The technology may be used in many indoor applications. The specific presentation of VLC in this study is with the use of light emitting diodes (LEDs) as the medium for transmission. Digital information will be sent through the LEDs as light pulses, and then a receiver will be able to collect the light pulses as a code and translate it to a corresponding audio data. In this study, the visible light communication system uses modulation schemes, such as on-off keying, so that the digital HIGHs and LOWs are representations of the binary code to be transmitted. Acknowledgement lights incorporated in the receiver are also utilized to make multicasting possible, and to signal that transmission is successful. © 2015 IEEE

Embodied uncertainty: living with complexity and natural hazards

In this paper, we examine the concept of embodied uncertainty by exploring multiple dimensions of uncertainty in the context of risks associated with extreme natural hazards. We highlight a need for greater recognition, particularly by disaster management and response agencies, of uncertainty as a subjective experience for those living at risk. Embodied uncertainty is distinguished from objective uncertainty by the nature of its internalisation at the individual level, where it is subjective, felt and directly experienced. This approach provides a conceptual pathway that sharpens knowledge of the processes that shape how individuals and communities interpret and contextualise risk. The ways in which individual characteristics, social identities and lived experiences shape interpretations of risk are explored by considering embodied uncertainty in four contexts: social identities and trauma, the co-production of knowledge, institutional structures and policy and long-term lived experiences. We conclude by outlining the opportunities that this approach presents, and provide recommendations for further research on how the concept of embodied uncertainty can aid decision-making and the management of risks in the context of extreme natural hazards